Question: Assembly of 454 raw data (in fastq)
0
gravatar for bird77
2.8 years ago by
bird7760
bird7760 wrote:

I need to assemble raw reads from a project that already has been published. The metagenome was sequenced with 454, but the files are only present in fastq format.

Is there an assembler which is up-to-date which can assemble long 454 reads with this quality profile? Can UDBA or Megahit deal with that?

Or does anyone have different recommendations?

Thank you for your help.

assembly • 1.1k views
ADD COMMENTlink modified 2.8 years ago by colindaven2.5k • written 2.8 years ago by bird7760

I thought (though I may well be wrong) that Velvet or SOAP was originally developed for 454 sequencing.

ADD REPLYlink written 2.8 years ago by Joe18k
0
gravatar for colindaven
2.8 years ago by
colindaven2.5k
Hannover Medical School
colindaven2.5k wrote:

Newbler always worked pretty well with 454. Otherwise CLC genomics was also easy.

Can Spades deal with it for a more modern option ?

ADD COMMENTlink written 2.8 years ago by colindaven2.5k

I don't think so. I use SPAdes fairly frequently and never noticed any information suggesting it does, but I am guessing a bit.

ADD REPLYlink written 2.8 years ago by Joe18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1123 users visited in the last hour